R Notebook

T cell prognostic

Lynch-like subgroup

Misc other

no real overall trends

CD8 stuff

#### clonality

All the T cell stuff

Because why not

Diversity

overall diversity

raw diversity

Change in diversity

Cell type diversity

this data is already log10(inv.simp)

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TM diversity

raw diversity

##  1-1  1-3 10-1 10-3 10-5 11-1 11-3 11-5 12-1 12-3 12-5 13-1 13-5 14-1 14-5 15-1 
##  469  372   53  104   79  144  134  212  122  353  565   74   88  402  407   73 
## 15-5 16-1 16-5 17-1 17-5 18-1 18-5 19-1 19-5  2-1  2-3  2-5 20-1 20-5 21-1 22-5 
##   77   86   79  236  271  198  373   82   80  180  143  145  138    9   28   53 
## 23-1 23-5 24-1 24-5  3-1  3-3  3-5  5-1  5-3  5-5  6-1  6-3  6-5  7-1  7-3  7-5 
##    1   84  255  245   28   21   28   91  270  377  327  286  124   35   45   18 
##  8-1  8-3  8-5  9-1  9-3  9-5 
##   23   14    9  210   52  127

Change in diversity

cell type diversity

this data is already log10(inv.simp)

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#### clonotype size rarefaction

spectratyping

overlap

similarity validation

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the pre-post tils always strong cluster in overlap/jaccard/morisita 26/9/3/12 consistent, 19 and 7 iffy (7 really low counts)

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morisita looks beautiful, all patients cluster really strongly some mixing with the low 20’s in jaccard and overlap, but overall very strong

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overlap is nearly perfect (just 3til and 3pbmc separate but still have an island of overlap out there), jaccard good but mixes some up, morisita segregates like all the til from nontil

temporal pbmc overlap

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yo jaccard ignores proportions/clones, just based off cdr3s

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pbmc-til overlap

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looks like generally stronger 5-7 overlap (but small and not much for any other)

the questionable data shows enrichment towards both extremes with outliers removed though, it looks like just increase in TM overlap for NLR

it kinda looked like something was there, but looks inconclusive

Clonotype cell types

this is erroring right now for me? 08.19 don’t have scaling worked out yet, and this is overall but treg lot of overlap cd4act cd8, cd8exh-act strong, cd4 act-exh?

not much clinical diff, maybe a bit more single in nr more 2+ in nr, more 2 in nlr/maybe l; the high nr outliers are 17

TEMRA distinctness

## [[1]]
## [[1]]$`CD8 TEMRA`
## [1] 78
## 
## [[1]]$Other
## [1] 1927
## 
## 
## [[2]]
## [[2]]$`CD8 TEMRA`
## [1] 57
## 
## [[2]]$Other
## [1] 1804
## 
## 
## [[3]]
## [[3]]$`CD8 TEMRA`
## [1] 11
## 
## [[3]]$Other
## [1] 1351
## 
## 
## [[4]]
## [[4]]$`CD8 TEMRA`
## [1] 51
## 
## [[4]]$Other
## [1] 2086
## 
## 
## [[5]]
## [[5]]$`CD8 TEMRA`
## [1] 36
## 
## [[5]]$Other
## [1] 2477
## 
## 
## [[6]]
## [[6]]$`CD8 TEMRA`
## [1] 57
## 
## [[6]]$Other
## [1] 2428
## 
## 
## [[7]]
## [[7]]$`CD8 TEMRA`
## [1] 85
## 
## [[7]]$Other
## [1] 1682
## 
## 
## [[8]]
## [[8]]$`CD8 TEMRA`
## [1] 128
## 
## [[8]]$Other
## [1] 3636
## 
## 
## [[9]]
## [[9]]$`CD8 TEMRA`
## [1] 15
## 
## [[9]]$Other
## [1] 1407
## 
## 
## [[10]]
## [[10]]$`CD8 TEMRA`
## [1] 41
## 
## [[10]]$Other
## [1] 3290
## 
## 
## [[11]]
## [[11]]$`CD8 TEMRA`
## [1] 75
## 
## [[11]]$Other
## [1] 6180
## 
## 
## [[12]]
## [[12]]$`CD8 TEMRA`
## [1] 43
## 
## [[12]]$Other
## [1] 1737
## 
## 
## [[13]]
## [[13]]$`CD8 TEMRA`
## [1] 68
## 
## [[13]]$Other
## [1] 2179
## 
## 
## [[14]]
## [[14]]$`CD8 TEMRA`
## [1] 170
## 
## [[14]]$Other
## [1] 1055
## 
## 
## [[15]]
## [[15]]$`CD8 TEMRA`
## [1] 134
## 
## [[15]]$Other
## [1] 1315
## 
## 
## [[16]]
## [[16]]$`CD8 TEMRA`
## [1] 50
## 
## [[16]]$Other
## [1] 2639
## 
## 
## [[17]]
## [[17]]$`CD8 TEMRA`
## [1] 41
## 
## [[17]]$Other
## [1] 2943
## 
## 
## [[18]]
## [[18]]$`CD8 TEMRA`
## [1] 55
## 
## [[18]]$Other
## [1] 1981
## 
## 
## [[19]]
## [[19]]$`CD8 TEMRA`
## [1] 57
## 
## [[19]]$Other
## [1] 1957
## 
## 
## [[20]]
## [[20]]$`CD8 TEMRA`
## [1] 197
## 
## [[20]]$Other
## [1] 799
## 
## 
## [[21]]
## [[21]]$`CD8 TEMRA`
## [1] 189
## 
## [[21]]$Other
## [1] 975
## 
## 
## [[22]]
## [[22]]$`CD8 TEMRA`
## [1] 42
## 
## [[22]]$Other
## [1] 466
## 
## 
## [[23]]
## [[23]]$`CD8 TEMRA`
## [1] 58
## 
## [[23]]$Other
## [1] 932
## 
## 
## [[24]]
## [[24]]$`CD8 TEMRA`
## [1] 94
## 
## [[24]]$Other
## [1] 1702
## 
## 
## [[25]]
## [[25]]$`CD8 TEMRA`
## [1] 89
## 
## [[25]]$Other
## [1] 2732
## 
## 
## [[26]]
## [[26]]$`CD8 TEMRA`
## [1] 125
## 
## [[26]]$Other
## [1] 2323
## 
## 
## [[27]]
## [[27]]$`CD8 TEMRA`
## [1] 90
## 
## [[27]]$Other
## [1] 2416
## 
## 
## [[28]]
## [[28]]$`CD8 TEMRA`
## [1] 104
## 
## [[28]]$Other
## [1] 1876
## 
## 
## [[29]]
## [[29]]$`CD8 TEMRA`
## [1] 96
## 
## [[29]]$Other
## [1] 1530
## 
## 
## [[30]]
## [[30]]$`CD8 TEMRA`
## [1] 28
## 
## [[30]]$Other
## [1] 60
## 
## 
## [[31]]
## [[31]]$`CD8 TEMRA`
## [1] 77
## 
## [[31]]$Other
## [1] 2664
## 
## 
## [[32]]
## [[32]]$`CD8 TEMRA`
## [1] 70
## 
## [[32]]$Other
## [1] 2951
## 
## 
## [[33]]
## [[33]]$`CD8 TEMRA`
## [1] 62
## 
## [[33]]$Other
## [1] 3290
## 
## 
## [[34]]
## [[34]]$`CD8 TEMRA`
## [1] 62
## 
## [[34]]$Other
## [1] 2710
## 
## 
## [[35]]
## [[35]]$`CD8 TEMRA`
## [1] 75
## 
## [[35]]$Other
## [1] 1792
## 
## 
## [[36]]
## [[36]]$`CD8 TEMRA`
## [1] 163
## 
## [[36]]$Other
## [1] 1184
## 
## 
## [[37]]
## [[37]]$`CD8 TEMRA`
## [1] 117
## 
## [[37]]$Other
## [1] 1538
## 
## 
## [[38]]
## [[38]]$`CD8 TEMRA`
## [1] 25
## 
## [[38]]$Other
## [1] 377
## 
## 
## [[39]]
## [[39]]$`CD8 TEMRA`
## [1] 85
## 
## [[39]]$Other
## [1] 2003
## 
## 
## [[40]]
## [[40]]$`CD8 TEMRA`
## [1] 109
## 
## [[40]]$Other
## [1] 4644
## 
## 
## [[41]]
## [[41]]$`CD8 TEMRA`
## [1] 111
## 
## [[41]]$Other
## [1] 2593
## 
## 
## [[42]]
## [[42]]$`CD8 TEMRA`
## [1] 95
## 
## [[42]]$Other
## [1] 2792
## 
## 
## [[43]]
## [[43]]$`CD8 TEMRA`
## [1] 73
## 
## [[43]]$Other
## [1] 1113
## 
## 
## [[44]]
## [[44]]$`CD8 TEMRA`
## [1] 110
## 
## [[44]]$Other
## [1] 1797
## 
## 
## [[45]]
## [[45]]$`CD8 TEMRA`
## [1] 101
## 
## [[45]]$Other
## [1] 2186
## 
## 
## [[46]]
## [[46]]$`CD8 TEMRA`
## [1] 48
## 
## [[46]]$Other
## [1] 517
## 
## 
## [[47]]
## [[47]]$`CD8 TEMRA`
## [1] 68
## 
## [[47]]$Other
## [1] 2155
## 
## 
## [[48]]
## [[48]]$`CD8 TEMRA`
## [1] 219
## 
## [[48]]$Other
## [1] 1542
## 
## 
## [[49]]
## [[49]]$`CD8 TEMRA`
## [1] 90
## 
## [[49]]$Other
## [1] 1667
## 
## 
## [[50]]
## [[50]]$`CD8 TEMRA`
## [1] 63
## 
## [[50]]$Other
## [1] 2002
## 
## 
## [[51]]
## [[51]]$`CD8 TEMRA`
## [1] 26
## 
## [[51]]$Other
## [1] 854
## 
## 
## [[52]]
## [[52]]$`CD8 TEMRA`
## [1] 54
## 
## [[52]]$Other
## [1] 1741
## 
## 
## [[53]]
## named list()
## 
## [[54]]
## named list()
## 
## [[55]]
## named list()
## 
## [[56]]
## named list()
## 
## [[57]]
## named list()
## 
## [[58]]
## named list()
## 
## [[59]]
## named list()
## 
## [[60]]
## named list()
## 
## [[61]]
## named list()

still not entirely sure about the mechanics of vegdist could still be a size effect of the temra, haven’t done downsampling also mean or median for the column version?

Cell counts

got some interesting ones, 25 is just 14, 15 strong 23/5, 23-1 is just 6 cells, 21-1 is 200 cells specific clusts - 3 (l high - temra right),8 (nlr lo - cd8 naive), 12 (nlr hi, cd4 activated ish, center top), 16 (nlr hi - dead?), 18(nlr hi,l lo, cd4 naive),21 (nlr hi - cd4 early?), 24 (l lo,cd8-4 transition), 29 (l lo - left gdt), ldat clusts - 4(nlr lo-cd14mono),9(nlr hi-cd16 mono),19(l lo-cdc),21(nlr hi-cd16nk.2),22(l lo-cd56 nk),26(nlr hi-pdc),28(l lo,nlr hi-mono??),29(l hi-plasma),31(l lo-progenitor),32(l lo-b/mono)

Proportion TM

## [[1]]

## 
## [[2]]

## 
## [[3]]

Lynch has higher prop of clones TM, decreases over time

## [[1]]

## 
## [[2]]

## 
## [[3]]

lynch highest prop TM, NLR second NLR is a lot more TM porpotion increase while others decrease But none of this translates to any pattern in change in TM clonality this could also be the result of sample size of pbmc and til - manual jaccard is better?

could do proportion of TMs for each by cell type or proportional composition of TMs for clinical by cell type and then uhhh raref TMs or actually that’s more div stuff